new type histogram view in particle analysis (04b35ae2) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+22 −77

Original line number	Diff line number	Diff line
		@@ -30,7 +30,7 @@ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
		from matplotlib.figure import Figure
		from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar

		from .analysiswidgets import ExpExcelDialog, AdditiveViewer
		from .analysiswidgets import ExpExcelDialog, AdditiveViewer, ParticleTypeView
		from .loadresults import LoadWITecResults
		from .particleeditor import ParticleEditor
		from .database import DataBaseWindow
		@@ -67,11 +67,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.currentSpectrumIndex = 0
		self.lastSpectrumInFocus = None

		self.typeHistogramCanvas = FigureCanvas(Figure())
		self.typeHistogram = ParticleTypeView(self)
		self.typeHistogram.indexClicked.connect(self.getAdditivePlot)
		self.sizeHistogramCanvas = FigureCanvas(Figure())

		self.typeHist_ax = self.typeHistogramCanvas.figure.subplots()
		self.typeHist_ax.axis('off')
		sizeHistGroup = QtWidgets.QGroupBox()
		sizeHistLayout = QtWidgets.QHBoxLayout()
		self.sizeHist_ax = self.sizeHistogramCanvas.figure.subplots()
		@@ -107,7 +106,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		splitter1.addWidget(sizeHistGroup)
		splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
		splitter2.addWidget(splitter1)
		splitter2.addWidget(self.typeHistogramCanvas)
		splitter2.addWidget(self.typeHistogram)
		splitter2.setSizes([300, 150])

		self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
		@@ -343,11 +342,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.importWindow = LoadWITecResults(self.datastats, self)
		self.importWindow.exec()

		def getAdditivePlot(self, event):
		clickedindex = int(np.round(event.xdata))
		@QtCore.pyqtSlot(int)
		def getAdditivePlot(self, clickedindex):
		polymer = self.datastats.typehistogram[clickedindex][0] #get the polymer name, that was clicked on

		if len(self.datastats.sorted_additives[clickedindex]) > 0:
		if self.datastats.sorted_additives is not None and \
		len(self.datastats.sorted_additives[clickedindex]) > 0:
		self.additivePlot = AdditiveViewer(polymer, self.datastats.sorted_additives[clickedindex])
		self.additivePlot.show()

		@@ -419,10 +419,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		self.menuLayout.addWidget(self.resultScrollarea)

		if self.datastats.currentAdditives is not None:
		self.typeHistogramCanvas.setCursor(QtGui.QCursor(QtCore.Qt.WhatsThisCursor))
		self.typeHistogramCanvas.mpl_connect('button_press_event', self.getAdditivePlot)

		self.expExcelAct.setDisabled(False)
		if sqlEnabled:
		self.expSQLAct.setDisabled(False)
		@@ -568,37 +564,15 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.updateSpecPlot()

		def updateHistogram(self):
		self.sizeHist_ax.clear()
		self.typeHist_ax.clear()

		self.typeHist_ax.axis('on')
		self.sizeHist_ax.axis('on')

		#draw the general histogram
		colorList = []
		if self.selOverlayAct.isChecked():
		abundancyList = []
		for index, checkbox in enumerate(self.polymerCheckBoxes):
		if checkbox.isChecked():
		abundancyList.append(self.datastats.typehistogram[index][1])
		curColor = self.getColorFromName(self.datastats.typehistogram[index][0], base255 = False)
		colorList.append(curColor)

		else:
		abundancyList = [i[1] for i in self.datastats.typehistogram]
		for polymer in self.datastats.typehistogram:
		curColor = self.getColorFromName(polymer[0], base255 = False)
		colorList.append(curColor)

		self.typeHist_ax.barh(range(len(abundancyList)), abundancyList, color=colorList)
		itemsInPlot = (len(abundancyList) if len(abundancyList) < self.dispResultSpinBox.value() else self.dispResultSpinBox.value())
		self.typeHist_ax.set_ylim([itemsInPlot, -1]) #plot in inverse order (have index 0 (highest abundancy) at top)

		###add text labels
		self.histPlotTextLabels = []
		y_label_position = 0
		labelList = []
		for index, i in enumerate(self.datastats.typehistogram):
		if not self.selOverlayAct.isChecked() or self.polymerCheckBoxes[index].isChecked():
		abundancyList.append(self.datastats.typehistogram[index][1])
		curColor = self.getColorFromName(self.datastats.typehistogram[index][0])
		colorList.append(QtGui.QColor(*curColor))
		if self.datastats.sorted_additives is None:
		numads = ''
		else:
		@@ -609,46 +583,17 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		numads = '(' + str(numads) + ')'
		numpolymers = i[1]
		label = ('{} x ' + self.datastats.typehistogram[index][0] + ' {}').format(numpolymers, numads)
		x_label_position = self.typeHist_ax.get_xlim()[1]*0.05
		self.histPlotTextLabels.append(self.typeHist_ax.text(x_label_position, y_label_position, label, fontsize = 15, rotation = 0, verticalalignment = 'bottom'))
		y_label_position += 1

		for label in self.histPlotTextLabels:
		pos = label.get_position()
		curLimits = self.typeHist_ax.get_ylim()
		if curLimits[1] < pos[1] < curLimits[0]:
		label.set_alpha(1)
		else:
		label.set_alpha(0)

		self.typeHist_ax.set_title('Polymer Type Distribution', fontsize = 15)
		self.typeHist_ax.tick_params(axis='y', which='both', left=False, labelleft=False)
		self.typeHist_ax.tick_params(axis='both', which='both', labelsize=15)
		self.typeHist_ax.set_ylabel('Polymer Type', fontsize = 15)
		self.typeHist_ax.set_xlabel('Number', fontsize = 15)

		if len(self.datastats.typehistogram) > self.dispResultSpinBox.value():

		def wheelScroll(event):
		step = -0.05event.stepself.dispResultSpinBox.value()
		ymin, ymax = self.typeHist_ax.get_ylim()
		if ymin > ymax:
		ymin, ymax = ymax, ymin
		self.typeHist_ax.set_ylim([ymax+step, ymin+step])

		for label in self.histPlotTextLabels:
		pos = label.get_position()
		if ymin+step < pos[1] < ymax+step:
		label.set_alpha(1)
		else:
		label.set_alpha(0)
		self.typeHist_ax.figure.canvas.draw()

		self.typeHistogramCanvas.mpl_connect('scroll_event', wheelScroll)
		labelList.append(label)

		self.typeHist_ax.figure.canvas.draw()
		print("abundancyList:", abundancyList)
		print("labelList:", labelList)
		print("colorList:", colorList)
		self.typeHistogram.updateTypes(list(zip(abundancyList, labelList, colorList)))

		#general size histogram
		self.sizeHist_ax.clear()
		self.sizeHist_ax.axis('on')

		self.bins = np.logspace(0.1, 3, 20)
		self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.getParticleStats()] #extract long size (if ellipse fit is nan -> box fit)
		sizehist = np.histogram(self.sizes, self.bins)

analysis/analysiswidgets.py

+72 −2

Original line number	Diff line number	Diff line
		@@ -19,7 +19,7 @@ along with this program, see COPYING.
		If not, see <https://www.gnu.org/licenses/>.
		"""

		from PyQt5 import QtWidgets
		from PyQt5 import QtWidgets, QtGui, QtCore
		import numpy as np
		import pandas as pd
		import os
		@@ -202,3 +202,73 @@ class AdditiveViewer(QtWidgets.QWidget):
		self.ax.hist(sortedAdditives)
		self.ax.set_ylabel('Number', fontsize = 15)
		self.ax.tick_params(axis='both', which='both', labelsize=15)


		class ParticleIndicator(QtWidgets.QPushButton):
		def __init__(self, number, numtotal, color, text, parent=None):
		super().__init__(parent)
		self.number = number
		self.numtotal = numtotal
		self.color = color
		self.text = text
		self.setFixedHeight(30)

		def paintEvent(self, event):
		r = self.number/self.numtotal
		width = self.width()
		height = self.height()

		qp = QtGui.QPainter()
		qp.begin(self)
		qp.fillRect(self.rect(), QtCore.Qt.white)
		qp.setPen(self.color)
		qp.setBrush(self.color)
		qp.drawRoundedRect(0, 0, int(width*r), height, 5. ,5.)
		qp.setPen(QtCore.Qt.black)
		qp.setBrush(QtCore.Qt.NoBrush)
		qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
		qp.drawText(self.rect(), QtCore.Qt.AlignLeft\|QtCore.Qt.AlignVCenter,
		self.text)

		qp.end()


		class ParticleTypeView(QtWidgets.QScrollArea):
		indexClicked = QtCore.pyqtSignal(int)
		def __init__(self, parent=None):
		super().__init__(parent)
		self.view = QtWidgets.QWidget(self)
		self.view.setCursor(QtGui.QCursor(QtCore.Qt.WhatsThisCursor))
		self.view.setMinimumWidth(250)

		group = QtWidgets.QGroupBox('Polymer Type Distribution', self.view)
		self.indicatorbox = QtWidgets.QVBoxLayout()
		self.indicatorbox.setContentsMargins(5,5,5,5)
		group.setLayout(self.indicatorbox)

		hbox = QtWidgets.QHBoxLayout()
		hbox.addWidget(group)
		self.view.setLayout(hbox)
		self.setWidgetResizable(True)
		self.setWidget(self.view)
		self.setAlignment(QtCore.Qt.AlignHCenter)

		def updateTypes(self, types):
		print("Updating polymer type view", flush=True)
		for i in range(self.indicatorbox.count()):
		self.indicatorbox.takeAt(0)

		numtotal = sum([num for num, text, color in types])

		def getIndexFunction(index):
		return lambda : self.indexClicked.emit(index)

		for index, entry in enumerate(types):
		num, text, color = entry
		print("num, text, color:", num, text, color, flush=True)
		pi = ParticleIndicator(num, numtotal, color, text)
		self.indicatorbox.addWidget(pi)
		pi.clicked.connect(getIndexFunction(index))
		self.indicatorbox.addStretch()
		self.view.update()

		No newline at end of file